Could I use a dyno tuned Stage 2/3 for my current setup then just re-tune as I add my turbo mods? Yes
Can I use the same engine managment as my project evolves w/o having to buy additional programs? No, you must buy the Boost upgrade when you go boost. (or before if you wish).
Is it worth the conversion from non-obd to obd1 so taht I can use the s200? Absolutly. Stage X Hondata's are being phased out I believe, so it would be in your best interest to go with the S200 system, and upgrade to S200b (for 250 bucks) later down the road. Although the upgrade to obd1 will add to the expence, it simply makes sense that you would utilize the latest in Hondata technology.
Hope I helped.